FastQC Summary

Summary statistics for all libraries
Filename Total Flagged As Poor Quality Sequence Length %GC
G1_KI_R1_cleanq.fq.gz 17,052,219 0 30-145 42
G1_KI_R2_cleanq.fq.gz 17,052,219 0 30-145 44
G2_KI_R1_cleanq.fq.gz 16,646,818 0 30-145 40
G2_KI_R2_cleanq.fq.gz 16,646,818 0 30-145 43
G3_KI_R1_cleanq.fq.gz 15,334,061 0 30-145 41
G3_KI_R2_cleanq.fq.gz 15,334,061 0 30-145 43
G4_KI_R1_cleanq.fq.gz 15,907,219 0 30-145 41
G4_KI_R2_cleanq.fq.gz 15,907,219 0 30-145 44
G5_KI_R1_cleanq.fq.gz 15,436,157 0 30-145 39
G5_KI_R2_cleanq.fq.gz 15,436,157 0 30-145 42
G6_KI_R1_cleanq.fq.gz 70,869,877 0 30-120 45
G6_KI_R2_cleanq.fq.gz 70,869,877 0 30-120 45
G7_KI_R1_cleanq.fq.gz 73,011,193 0 30-120 45
G7_KI_R2_cleanq.fq.gz 73,011,193 0 30-120 45
G8_KI_R1_cleanq.fq.gz 16,920,350 0 30-145 41
G8_KI_R2_cleanq.fq.gz 16,920,350 0 30-145 44

Read Totals

Library Sizes ranged between 15,334,061 and 73,011,193 reads.

Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.

FastQC Summary

Summary of FastQC flags for each parameter

Per Base Sequence Quality

Heatmap showing mean base qualities for each library

Per Sequence Quality Scores

Heatmap showing mean sequence qualities for each library

Per Base Sequence Content

Heatmap of summed base distributions along each read

Per Sequence GC Content

GC Content Heatmap normalised to theoretical GC content in the Hsapiens Transcriptome

GC Content Distributions for all reads showing theoretical GC content from the Hsapiens Transcriptome

Sequence Length Distribution

Sequence Duplication Levels

Adapter Content

Universal Adapter Content

Overrepresented Summary

Total overrepresented sequences for each library

Overrepresented Sequences

## `summarise()` has grouped output by 'Sequence'. You can override using the `.groups` argument.
Summary of the most overrepresented sequences in all files. A maximum of 30 sequences are shown
Sequence Total Present In Overall Percentage Max_Percentage Possible_Source
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 4,521,105 12 0.93729672% 4.945363% No Hit
TGGGGCTATTTGACCTGACTGTCAGACTTCTAGCTCTAGCAAGGACTCCT 3,000,084 6 0.62196496% 5.423867% No Hit
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2,836,180 12 0.58798507% 3.229398% No Hit
GCTATTTGACCTGACTGTCAGACTTCTAGCTCTAGCAAGGACTCCTGCAC 1,717,227 6 0.35600837% 2.998775% No Hit
TGGGGACCAAAGAACTTCTGGAGAACTCGCAAGACTTCTTCAATCTTTCA 963,277 6 0.19970259% 1.398090% No Hit
GACCAAAGAACTTCTGGAGAACTCGCAAGACTTCTTCAATCTTTCAACAC 585,611 6 0.12140644% 0.800140% No Hit
TCTGCCCAGCATGTTTCCACATTCTACATTTCTAAGTGAATGGCTCTGCA 562,043 2 0.11652042% 0.525591% No Hit
AAGGTGCAGCTACCACGGGCCTGGCCGCAAGCAAGTGTATCAGCAGCGGG 538,545 2 0.11164891% 0.521687% No Hit
TGGGGCACCAAAGAACTTCTGGAGAACTCGCAAGACTTCTTCAATCTTTC 439,899 6 0.09119803% 0.808370% No Hit
TGGGCTATTTGACCTGACTGTCAGACTTCTAGCTCTAGCAAGGACTCCTG 381,277 6 0.07904477% 0.698660% No Hit
TGGGGATCCACCAAAGAACTTCTGGAGAACTCGCAAGACTTCTTCAATCT 377,593 6 0.07828101% 0.584183% No Hit
GTCAGACTTCTAGCTCTAGCAAGGACTCCTGCACTAAGCTTCAGCCATGA 325,488 2 0.06747882% 0.299757% No Hit
TTTTCAGAGGTGCCTCTGCATGGTCCGAAGGTGCAGCTACCACGGGCCTG 310,383 2 0.06434732% 0.268862% No Hit
TTTCAGAGGTGCCTCTGCATGGTCCGAAGGTGCAGCTACCACGGGCCTGG 274,615 2 0.05693204% 0.254067% No Hit
GCACCAAAGAACTTCTGGAGAACTCGCAAGACTTCTTCAATCTTTCAACA 265,176 6 0.05497519% 0.464424% No Hit
CAGACTTCTAGCTCTAGCAAGGACTCCTGCACTAAGCTTCAGCCATGAGG 234,346 2 0.04858364% 0.218258% No Hit
CTATTTGACCTGACTGTCAGACTTCTAGCTCTAGCAAGGACTCCTGCACT 224,163 6 0.04647254% 0.399548% No Hit
GATCCACCAAAGAACTTCTGGAGAACTCGCAAGACTTCTTCAATCTTTCA 221,696 6 0.04596109% 0.322719% No Hit
AAGAAGGTTAGGTTGACACCGGCAAATATGACGCCAAATTGAATTTTTGT 196,139 2 0.04066272% 0.159445% No Hit
TGGGACCAAAGAACTTCTGGAGAACTCGCAAGACTTCTTCAATCTTTCAA 152,125 5 0.03153792% 0.247681% No Hit
GATGTTTTCAGAGGTGCCTCTGCATGGTCCGAAGGTGCAGCTACCACGGG 147,708 1 0.03062221% 0.202309% No Hit
TTCTATGGGGACTACTATGCGGTGATCTACTTCTAGCAGACGAAGGTGGC 138,486 1 0.02871034% 0.189678% No Hit
ACTGCCAGGAGAAAAAGGATTGGCCATCAAGATGTAGGTTCTGGGTTCAA 134,254 1 0.02783298% 0.189437% No Hit
ACTGCCAGGAGAAAATGGATTGGCCATCAAGATGTAGGTTCTGGGTTCAA 133,483 1 0.02767314% 0.182825% No Hit
GGATCCTCTTCCTTCTCTTTACCATCTTTTTGGTCTTCTACCAAGCTGCT 117,186 1 0.02429452% 0.160504% No Hit
TGGGGAGAGACCATCCTCTAAGAGCAGCTCTCCCTCTGTCGCCTTAGACC 112,761 1 0.02337714% 0.730499% No Hit
TGGGGAGAGCCTGGTTCTTGCTTCAACAGTGCTTGAACGGAGCCGGTTCT 108,211 5 0.02243386% 0.146514% No Hit
TGGGGACCAAAGAACTTCTGGAGAACTCGCAAGACTTCTTCAACCTTTCA 104,519 1 0.02166845% 0.657054% No Hit
TTGTTGATTTCGTCTATAAGATAAAGGATGCGGAGGGAGGGGAGGGCAAT 92,844 1 0.01924803% 0.127164% No Hit
GTTCGGCTTCCAAGACGCAGCATCACCAATCATAGAAGAGCTTTTACACT 86,667 1 0.01796744% 0.118704% No Hit

Session Information

R version 3.6.1 (2019-07-05)

Platform: x86_64-w64-mingw32/x64 (64-bit)

locale: LC_COLLATE=English_Australia.1252, LC_CTYPE=English_Australia.1252, LC_MONETARY=English_Australia.1252, LC_NUMERIC=C and LC_TIME=English_Australia.1252

attached base packages: parallel, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: readr(v.1.4.0), stringr(v.1.4.0), magrittr(v.2.0.1), scales(v.1.1.1), pander(v.0.6.3), kableExtra(v.1.3.4), dplyr(v.1.0.6), ngsReports(v.1.2.0), tibble(v.3.1.1), ggplot2(v.3.3.2) and BiocGenerics(v.0.32.0)

loaded via a namespace (and not attached): bitops(v.1.0-7), matrixStats(v.0.58.0), lubridate(v.1.7.10), RColorBrewer(v.1.1-2), webshot(v.0.5.2), httr(v.1.4.2), GenomeInfoDb(v.1.22.1), tools(v.3.6.1), utf8(v.1.2.1), R6(v.2.5.1), DT(v.0.19), DBI(v.1.1.1), lazyeval(v.0.2.2), colorspace(v.2.0-1), withr(v.2.4.2), tidyselect(v.1.1.1), compiler(v.3.6.1), rvest(v.1.0.1), Biobase(v.2.46.0), flashClust(v.1.01-2), xml2(v.1.3.2), DelayedArray(v.0.12.3), plotly(v.4.9.4.1), ggdendro(v.0.1.22), labeling(v.0.4.2), systemfonts(v.1.0.2), digest(v.0.6.25), Rsamtools(v.2.2.3), rmarkdown(v.2.11), svglite(v.2.0.0), XVector(v.0.26.0), jpeg(v.0.1-8.1), pkgconfig(v.2.0.3), htmltools(v.0.5.0), highr(v.0.9), FactoMineR(v.2.4), htmlwidgets(v.1.5.4), rlang(v.0.4.11), rstudioapi(v.0.13), farver(v.2.1.0), jquerylib(v.0.1.4), generics(v.0.1.0), hwriter(v.1.3.2), zoo(v.1.8-9), jsonlite(v.1.7.2), crosstalk(v.1.1.1), BiocParallel(v.1.20.1), RCurl(v.1.98-1.3), GenomeInfoDbData(v.1.2.2), leaps(v.3.1), Matrix(v.1.2-18), Rcpp(v.1.0.5), munsell(v.0.5.0), S4Vectors(v.0.24.4), fansi(v.0.4.2), lifecycle(v.1.0.1), scatterplot3d(v.0.3-41), stringi(v.1.6.1), yaml(v.2.2.1), MASS(v.7.3-51.6), SummarizedExperiment(v.1.16.1), zlibbioc(v.1.32.0), plyr(v.1.8.6), grid(v.3.6.1), ggrepel(v.0.9.1), crayon(v.1.4.1), lattice(v.0.20-41), Biostrings(v.2.54.0), hms(v.1.1.1), knitr(v.1.29), pillar(v.1.6.3), GenomicRanges(v.1.38.0), reshape2(v.1.4.4), stats4(v.3.6.1), glue(v.1.4.2), evaluate(v.0.14), ShortRead(v.1.44.3), latticeExtra(v.0.6-29), data.table(v.1.14.0), png(v.0.1-7), vctrs(v.0.3.8), gtable(v.0.3.0), purrr(v.0.3.4), tidyr(v.1.1.3), assertthat(v.0.2.1), xfun(v.0.26), viridisLite(v.0.4.0), truncnorm(v.1.0-8), GenomicAlignments(v.1.22.1), IRanges(v.2.20.2), cluster(v.2.1.0) and ellipsis(v.0.3.2)